Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1792
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 59349
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:5944 original size:22 final size:22
Alignment explanation
Indices: 5916--5959 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
5906 TTTTGAACCA
5916 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
5938 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
5960 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:12386 original size:21 final size:22
Alignment explanation
Indices: 12362--12406 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
12352 AGAAAAAGAG
*
12362 AAATACAAAAA-AGAATAG-ATC
1 AAAT-CAAAAAGAAAATAGAATC
12383 AAATCAAAAAGAAAATAGAATC
1 AAATCAAAAAGAAAATAGAATC
12405 AA
1 AA
12407 CAATTTGCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 10 0.48
22 5 0.24
ACGTcount: A:0.69, C:0.09, G:0.09, T:0.13
Consensus pattern (22 bp):
AAATCAAAAAGAAAATAGAATC
Found at i:15244 original size:35 final size:35
Alignment explanation
Indices: 15195--15369 Score: 239
Period size: 35 Copynumber: 5.1 Consensus size: 35
15185 GTCCAAAAAG
* *
15195 AAATAATACATGAACAGGAGAGATTCCCTGCAACA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
*
15230 AAATAATGTGTGAACAGGAGAGATTCCCTGCAACA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
*
15265 AAATAATGCGTGAACAGGAGAGATTCCCTGCAA-G
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
* *
15299 AAATGAT--GTGAACAGGAAAGATTCCCTGCAACA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
* * * *
15332 GAATAATGCGTGAACAGGAAATATTCCCTGCAAGA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
15367 AAA
1 AAA
15370 GACAAGTGAA
Statistics
Matches: 124, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
32 23 0.19
33 5 0.04
34 6 0.05
35 90 0.73
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (35 bp):
AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
Found at i:15337 original size:67 final size:68
Alignment explanation
Indices: 15195--15368 Score: 251
Period size: 67 Copynumber: 2.5 Consensus size: 68
15185 GTCCAAAAAG
* * * *
15195 AAATAATACATGAACAGGAGAGATTCCCTGCAACAAAATAATGTGTGAACAGGAGAGATTCCCTG
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAA-GAAATAA-GTGTGAACAGGAAAGATTCCCTG
15260 CAACA
64 CAACA
*
15265 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGA-TGTGAACAGGAAAGATTCCCTGCA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATAAGTGTGAACAGGAAAGATTCCCTGCA
15329 ACA
66 ACA
* * *
15332 GAATAATGCGTGAACAGGAAATATTCCCTGCAAGAAA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAA
15369 AGACAAGTGA
Statistics
Matches: 96, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
67 60 0.62
69 5 0.05
70 31 0.32
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (68 bp):
AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATAAGTGTGAACAGGAAAGATTCCCTGCA
ACA
Found at i:20032 original size:20 final size:22
Alignment explanation
Indices: 20002--20045 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
19992 AGAAAAAGAG
20002 AAATACAAAAA-AGAATAG-ATC
1 AAATACAAAAAGA-AATAGAATC
20023 AAAT-CAAAAAGAAATAGAATC
1 AAATACAAAAAGAAATAGAATC
20044 AA
1 AA
20046 CAATTTGCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.68, C:0.09, G:0.09, T:0.14
Consensus pattern (22 bp):
AAATACAAAAAGAAATAGAATC
Found at i:20959 original size:8 final size:9
Alignment explanation
Indices: 20938--20969 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
20928 AATCCCGCAA
20938 AAAAAAGTC
1 AAAAAAGTC
20947 AAAAAAGTC
1 AAAAAAGTC
*
20956 AAAAAAATC
1 AAAAAAGTC
20965 AAAAA
1 AAAAA
20970 TACGAAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.75, C:0.09, G:0.06, T:0.09
Consensus pattern (9 bp):
AAAAAAGTC
Found at i:24728 original size:20 final size:20
Alignment explanation
Indices: 24682--24728 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
24672 AGCTCGTTTC
*
24682 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
24702 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
24722 CAGCTCA
1 CAGCTCA
24729 ATTTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:38868 original size:19 final size:19
Alignment explanation
Indices: 38823--38869 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
38813 ACTCTCAATC
38823 TCTTTTTGCTCTTTTTCAT
1 TCTTTTTGCTCTTTTTCAT
* *
38842 TCTCTTTTTCT-TTTTTGATT
1 TCT-TTTTGCTCTTTTTCA-T
38862 TCTTTTTG
1 TCTTTTTG
38870 TGTCTTCCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.04, C:0.17, G:0.06, T:0.72
Consensus pattern (19 bp):
TCTTTTTGCTCTTTTTCAT
Found at i:42289 original size:22 final size:23
Alignment explanation
Indices: 42264--42312 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
42254 ATCAGCTTCT
42264 TTAATAC-ACCTATTAAGACACA
1 TTAATACGACCTATTAAGACACA
* *
42286 TTAA-ACGACTTATTAGGACACA
1 TTAATACGACCTATTAAGACACA
42308 TTAAT
1 TTAAT
42313 CATACCAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (23 bp):
TTAATACGACCTATTAAGACACA
Found at i:44037 original size:13 final size:13
Alignment explanation
Indices: 44019--44044 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44009 TGTGTCCTAA
44019 TATGAATTAAATT
1 TATGAATTAAATT
44032 TATGAATTAAATT
1 TATGAATTAAATT
44045 GCTTTCAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGAATTAAATT
Found at i:45173 original size:11 final size:11
Alignment explanation
Indices: 45157--45196 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
45147 GTAAGTGATT
45157 AAAAAAATTAA
1 AAAAAAATTAA
45168 AAAAAAATTGAA
1 AAAAAAATT-AA
*
45180 AAAAAAAGTAA
1 AAAAAAATTAA
45191 AAAAAA
1 AAAAAA
45197 TTCGTGGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.12
Consensus pattern (11 bp):
AAAAAAATTAA
Found at i:46172 original size:6 final size:6
Alignment explanation
Indices: 46147--46245 Score: 65
Period size: 6 Copynumber: 16.0 Consensus size: 6
46137 TAATGAATTC
** * * *
46147 GAAAAA GAAAGT GAAGAA GAAAAA GAAAACA -AAAAA GAAAAC GAAAAC
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAA-A GAAAAA GAAAAA GAAAAA
** * * *
46195 GAAAAA GTGAGA GAAAAA GAAAAT GAAGAAAA GAAAATT GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA G-A-AAAA GAAAA-A GAAAAA GAAAAA
46246 TATGAAAATG
Statistics
Matches: 70, Mismatches: 18, Indels: 10
0.71 0.18 0.10
Matches are distributed among these distances:
5 1 0.01
6 57 0.81
7 8 0.11
8 4 0.06
ACGTcount: A:0.72, C:0.03, G:0.20, T:0.05
Consensus pattern (6 bp):
GAAAAA
Found at i:46228 original size:14 final size:13
Alignment explanation
Indices: 46207--46244 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
46197 AAAAGTGAGA
46207 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
46219 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
46234 GAAAAAGAAAA
1 GAAAAAGAAAA
46245 ATATGAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:46284 original size:18 final size:18
Alignment explanation
Indices: 46263--46302 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
46253 ATGAGATTTC
46263 AAAAACAAAA-GAGAGTG
1 AAAAACAAAATGAGAGTG
*
46280 AAAAACAAAATGAGATTG
1 AAAAACAAAATGAGAGTG
46298 AAAAA
1 AAAAA
46303 GAAAGAGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.68, C:0.05, G:0.17, T:0.10
Consensus pattern (18 bp):
AAAAACAAAATGAGAGTG
Found at i:46285 original size:17 final size:17
Alignment explanation
Indices: 46263--46312 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
46253 ATGAGATTTC
46263 AAAAACAAAAGAGAGTG
1 AAAAACAAAAGAGAGTG
*
46280 AAAAACAAAATGAGATTG
1 AAAAACAAAA-GAGAGTG
*
46298 AAAAA-GAAAGAGAGT
1 AAAAACAAAAGAGAGT
46313 TTGAAAAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 5 0.17
17 13 0.45
18 11 0.38
ACGTcount: A:0.64, C:0.04, G:0.22, T:0.10
Consensus pattern (17 bp):
AAAAACAAAAGAGAGTG
Found at i:46316 original size:18 final size:17
Alignment explanation
Indices: 46270--46344 Score: 54
Period size: 18 Copynumber: 4.5 Consensus size: 17
46260 TTCAAAAACA
*
46270 AAAGAGAG-TGAAAAAC
1 AAAGAGAGTTGAAAAAG
46286 AAA-ATGAGATTGAAAAAG
1 AAAGA-GAG-TTGAAAAAG
46304 AAAGAGAGTTTG-AAAAG
1 AAAGAGAG-TTGAAAAAG
*
46321 AAA-ACGAG-TGAAGAAG
1 AAAGA-GAGTTGAAAAAG
46337 -AAGAGAGT
1 AAAGAGAGT
46345 GCTCAAACAC
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
15 8 0.17
16 12 0.25
17 11 0.23
18 16 0.33
19 1 0.02
ACGTcount: A:0.57, C:0.03, G:0.28, T:0.12
Consensus pattern (17 bp):
AAAGAGAGTTGAAAAAG
Found at i:47659 original size:11 final size:10
Alignment explanation
Indices: 47634--47694 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
47624 ACCAATAAAA
47634 TAAA-TGAGC
1 TAAATTGAGC
*
47643 TGAATTGTAGC
1 TAAATTG-AGC
47654 TAAATTGAGC
1 TAAATTGAGC
**
47664 TCGATTGAGC
1 TAAATTGAGC
47674 TGAAA-TGAGC
1 T-AAATTGAGC
*
47684 TCAATTGAGC
1 TAAATTGAGC
47694 T
1 T
47695 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:47695 original size:20 final size:20
Alignment explanation
Indices: 47635--47695 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
47625 CCAATAAAAT
*
47635 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
47655 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
47676 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
47696 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:49526 original size:13 final size:13
Alignment explanation
Indices: 49508--49533 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49498 TGTGTCCTAA
49508 TATGAATTAAATT
1 TATGAATTAAATT
49521 TATGAATTAAATT
1 TATGAATTAAATT
49534 GCTTTCAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGAATTAAATT
Found at i:50630 original size:22 final size:22
Alignment explanation
Indices: 50605--50655 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 22
50595 GTTTAATTAA
*
50605 GAAATGGATTTGG-TTTTGGTAC
1 GAAATGG-TATGGATTTTGGTAC
50627 GAAATGGTATGGAATTTTTGGTAC
1 GAAATGGTATGG-A-TTTTGGTAC
50651 GAAAT
1 GAAAT
50656 AAACCAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 4 0.16
22 7 0.28
24 14 0.56
ACGTcount: A:0.29, C:0.04, G:0.29, T:0.37
Consensus pattern (22 bp):
GAAATGGTATGGATTTTGGTAC
Found at i:55614 original size:22 final size:23
Alignment explanation
Indices: 55564--55614 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
55554 AATTTGGTTT
*
55564 ATTTCGTACCAAAAATTCCATACC
1 ATTTCGTACCAAAAA-TCCAAACC
55588 ATTTCGTACC-AAAA-CCAAATCC
1 ATTTCGTACCAAAAATCCAAA-CC
55610 ATTTC
1 ATTTC
55615 TTAATTAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 4 0.16
22 7 0.28
23 4 0.16
24 10 0.40
ACGTcount: A:0.37, C:0.29, G:0.04, T:0.29
Consensus pattern (23 bp):
ATTTCGTACCAAAAATCCAAACC
Found at i:58523 original size:13 final size:13
Alignment explanation
Indices: 58505--58530 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
58495 GTTGTCCTAA
58505 TATGAATTAAATT
1 TATGAATTAAATT
58518 TATGAATTAAATT
1 TATGAATTAAATT
58531 GCTTTCAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGAATTAAATT
Done.